I don't know about timelines or any of that, but when I played the game (I was very young at the time, like in elementary school) I always thought that child link traveled into another world/dimension and the link in that dimension/world was dead, thus you could use the Fierce Deity (Spellcheck?) mask in the same way you could for the Zora, Goron, and Deku masks. At the time I just figured in order for you to transform, the mask had to contain the soul of dead person or something like that.